I have an '03, and just started getting this in Feb of 2014 about 5,000 miles after changing the timing belt (@ about 108,000 on vehicle). My immediate thoughts were that I had screwed something up when I changed the timing belt. I have since slowly gone back through everything I took apart and have ruled out errors in timing belt change.
Since ruling that out, I have:
-replaced all U-joints
-tires balanced
-replaced both front wheel bearings
-replaced rear drive shaft
-replaced both cv-axles
-replaced fr/rear differential fluid
-replaced serpentine belt tensioner... long shot
My latest change was installing Bilstein 5100's and FJ Cruiser coils, for a net lift of a little less than 3" up front. I've been running 285/70/17's for over two years and didn't have this issue until about 6 months ago. My next step was going to be a front differential overhaul, but it sounds like that may be a waste of time after reading through this thread since the issue is being diagnosed as harmonic. It has crossed my mind, and this thread supports it, to replace the crank pulley/harmonic balancer. Since the noise began somewhat shortly after having the crank pulley/balancer off the vehicle, the crank pulley has been on my list of things to replace or investigate. Has anybody else suffering from this issue gone down that road?
I've spent countless hours under my 4runner hoping to find that loose bolt/heat-shield/anything! It is driving me crazy. It is getting more severe- or at least I'm noticing it more. It's starting to remind me of my Jeep XJ days... I hate throwing parts at a problem instead of being able to diagnose->research->fix. If the problem is truly harmonic, it seems replacing the harmonic balancer would be an easy diagnosis & fix. Just wanted to see if anybody had tried that before dropping the money.